HAWC+ Data Cookbook / 30 Doradus Data Release¶


In this jupyter cookbook, we will explore the HAWC+ data cube and describe some of the basic analysis techniques involving imaging polarimetry data.

This cookbook follows the SOFIA press release of 30 Doradus observations: SOFIA Reveals Never-Before-Seen Magnetic Field Details.

The Level 4 reduced data from this program has been released immediately to the public and is available on the SOFIA Data Cycle System (DCS). This notebook will guide the reader through downloading the 30 Doradus data with a walkthrough of basic analysis techniques with python.

Downloading HAWC+ Data¶

SOFIA Data Organization¶

After downloading the SOFIA DCS bundle to your working directory you will want to unzip it, which will produce a directory structure like this:

.
└── sofia_data
    ├── level4
    │   └── p5813
    │       └── F0484_HA_POL_7600018_HAWCHWPC_PMP_022-114.fits
    └── missions
        ├── 2018-07-05_HA_F481
        │   └── p5827
        │       └── F0481_HA_POL_7600012_HAWDHWPD_PMP_050-083.fits
        ├── 2018-07-07_HA_F483
        │   └── p5646
        │       └── F0483_HA_POL_7600014_HAWCHWPC_PMP_022-065.fits
        ├── 2018-07-11_HA_F484
        │   └── p5648
        │       └── F0484_HA_POL_7600017_HAWCHWPC_PMP_065-114.fits
        └── 2018-07-12_HA_F485
            └── p5658
                ├── g1
                │   └── F0485_HA_POL_76000110_HAWAHWPA_PMP_043-052.fits
                └── g2
                    └── F0485_HA_POL_7600019_HAWEHWPE_PMP_055-075.fits

Note that each file represents observations with a different filter. However, two observations were made with the same filter (HAWC C, $89\,\mathrm{\mu m}$). These files, F0483_HA_POL_7600014_HAWCHWPC_PMP_022-065.fits and F0484_HA_POL_7600017_HAWCHWPC_PMP_065-114.fits, were combined into one: level4->p5813->F0484_HA_POL_7600018_HAWCHWPC_PMP_022-114.fits.

You can choose to keep the fits files nested, or copy them into one directory.

For the purpose of this basic analysis, though, let us dump all the files into one sofia_data directory:

.
└── sofia_data
    ├── F0481_HA_POL_7600012_HAWDHWPD_PMP_050-083.fits
    ├── F0483_HA_POL_7600014_HAWCHWPC_PMP_022-065.fits
    ├── F0484_HA_POL_7600017_HAWCHWPC_PMP_065-114.fits
    ├── F0484_HA_POL_7600018_HAWCHWPC_PMP_022-114.fits
    ├── F0485_HA_POL_76000110_HAWAHWPA_PMP_043-052.fits
    └── F0485_HA_POL_7600019_HAWEHWPE_PMP_055-075.fits

Data Structure¶

For this analysis, we require the standard numpy/scipy/matplotlib stack as well the astropy and aplpy modules.

With just a few lines of code, we can explore the HAWC+ fits data cubes and plot the images.

In [1]:
from astropy.io import fits

efile = 'sofia_data/F0485_HA_POL_7600019_HAWEHWPE_PMP_055-075.fits'
dfile = 'sofia_data/F0481_HA_POL_7600012_HAWDHWPD_PMP_050-083.fits'
cfile = 'sofia_data/F0484_HA_POL_7600018_HAWCHWPC_PMP_022-114.fits'


afile = 'sofia_data/F0485_HA_POL_76000110_HAWAHWPA_PMP_043-052.fits'
hawc = fits.open(afile)
hawc.info()
Filename: sofia_data/F0485_HA_POL_76000110_HAWAHWPA_PMP_043-052.fits
No.    Name      Ver    Type      Cards   Dimensions   Format
  0  STOKES I      1 PrimaryHDU     572   (94, 114)   float64   
  1  ERROR I       1 ImageHDU        27   (94, 114)   float64   
  2  STOKES Q      1 ImageHDU        18   (94, 114)   float64   
  3  ERROR Q       1 ImageHDU        18   (94, 114)   float64   
  4  STOKES U      1 ImageHDU        18   (94, 114)   float64   
  5  ERROR U       1 ImageHDU        18   (94, 114)   float64   
  6  IMAGE MASK    1 ImageHDU        27   (94, 114)   float64   
  7  PERCENT POL    1 ImageHDU        18   (94, 114)   float64   
  8  DEBIASED PERCENT POL    1 ImageHDU        18   (94, 114)   float64   
  9  ERROR PERCENT POL    1 ImageHDU        18   (94, 114)   float64   
 10  POL ANGLE     1 ImageHDU        18   (94, 114)   float64   
 11  ROTATED POL ANGLE    1 ImageHDU        18   (94, 114)   float64   
 12  ERROR POL ANGLE    1 ImageHDU        18   (94, 114)   float64   
 13  POL FLUX      1 ImageHDU        18   (94, 114)   float64   
 14  ERROR POL FLUX    1 ImageHDU        18   (94, 114)   float64   
 15  DEBIASED POL FLUX    1 ImageHDU        18   (94, 114)   float64   
 16  MERGED DATA    1 BinTableHDU    234   8R x 67C   [1J, 1E, 1E, 1E, 1E, 1E, 1E, 1E, 1E, 1J, 1J, 1E, 1K, 1K, 1J, 1E, 1E, 1J, 1E, 1E, 1E, 1E, 1E, 1E, 1B, 1E, 1E, 1E, 1E, 1E, 1E, 1D, 1D, 1D, 1D, 1D, 1D, 1D, 1D, 1D, 1D, 1D, 1D, 1D, 1D, 1D, 1J, 1D, 1J, 1D, 1D, 1D, 1J, 1J, 1J, 2624E, 2624E, 1E, 1J, 2624E, 2624E, 2624E, 2624E, D, D, D, 49A]   
 17  POL DATA      1 BinTableHDU     34   10716R x 10C   [J, J, D, D, D, D, D, D, D, D]   
 18  FINAL POL DATA    1 BinTableHDU     30   84R x 8C   [D, D, D, D, D, D, D, D]   

We can see above the data structure of the multi-extension fits files. Each file contains 19 extensions which encapsulates all of the Stokes parameters in a single package.


Stokes I¶

Stokes $I$---the zeroth extension in the fits file---represents the total intensity of the image, where $I^2 = Q^2 + U^2$.

Let us go ahead and plot this extension:

In [2]:
import matplotlib.pyplot as plt
%matplotlib notebook
# ^jupyter magic for inline plots
from aplpy import FITSFigure

# set colormap for all plots
cmap = 'rainbow'

stokes_i = hawc['STOKES I']               # or hawc[0]. Note the extension is from the hawc.info() table above

fig = plt.figure(figsize=(7,7))

axs = FITSFigure(stokes_i, figure=fig)    # load HDU into aplpy figure
axs.show_colorscale(cmap=cmap)            # display the data with WCS projection and chosen colormap

# FORMATTING
axs.set_tick_labels_font(size='small')
axs.set_axis_labels_font(size='small')

# Add colorbar
axs.add_colorbar()
axs.colorbar.set_axis_label_text('Flux (Jy/pix)')
/home/gordon/miniconda3/lib/python3.6/site-packages/mpl_toolkits/axes_grid/__init__.py:12: MatplotlibDeprecationWarning: 
The mpl_toolkits.axes_grid module was deprecated in Matplotlib 2.1 and will be removed two minor releases later. Use mpl_toolkits.axes_grid1 and mpl_toolkits.axisartist provies the same functionality instead.
  obj_type='module')
INFO: Auto-setting vmin to -9.832e-02 [aplpy.core]
INFO: Auto-setting vmax to  1.698e+00 [aplpy.core]
/home/gordon/miniconda3/lib/python3.6/site-packages/aplpy/normalize.py:115: RuntimeWarning: invalid value encountered in less
  negative = result < 0.

Stokes Q and U¶

Similarly, we can plot the Stokes Q and Stokes U images:

In [3]:
stokes_q = hawc['STOKES Q']
stokes_u = hawc['STOKES U']

axq = FITSFigure(stokes_q, subplot=(1,2,1))  # generate FITSFigure as subplot to have two axes together
axq.show_colorscale(cmap=cmap)               # show Q


axu = FITSFigure(stokes_u, subplot=(1,2,2),
                 figure=plt.gcf())
axu.show_colorscale(cmap=cmap)               # show U

# FORMATTING
axq.set_title('Stokes Q')
axu.set_title('Stokes U')
axu.axis_labels.set_yposition('right')
axu.tick_labels.set_yposition('right')
axq.set_tick_labels_font(size='small')
axq.set_axis_labels_font(size='small')
axu.set_tick_labels_font(size='small')
axu.set_axis_labels_font(size='small')
INFO: Auto-setting vmin to -6.959e-02 [aplpy.core]
INFO: Auto-setting vmax to  8.873e-02 [aplpy.core]
/home/gordon/miniconda3/lib/python3.6/site-packages/aplpy/normalize.py:115: RuntimeWarning: invalid value encountered in less
  negative = result < 0.
INFO: Auto-setting vmin to -6.281e-02 [aplpy.core]
INFO: Auto-setting vmax to  7.749e-02 [aplpy.core]


We can additionally plot the associated error maps for each extension.

In [4]:
stokes_q = hawc['STOKES Q']
error_q = hawc['ERROR Q']

axq = FITSFigure(stokes_q, subplot=(1,2,1))  # generate FITSFigure as subplot to have two axes together
axq.show_colorscale(cmap=cmap)               # show Q


axe = FITSFigure(error_q, subplot=(1,2,2), figure=plt.gcf())
axe.show_colorscale(cmap=cmap)               # show error

# FORMATTING
axq.set_title('Stokes Q')
axe.set_title('Error Q')
axq.axis_labels.hide()                       # hide axis/tick labels
axe.axis_labels.hide()
axq.tick_labels.hide()
axe.tick_labels.hide()
INFO: Auto-setting vmin to -6.959e-02 [aplpy.core]
INFO: Auto-setting vmax to  8.873e-02 [aplpy.core]
/home/gordon/miniconda3/lib/python3.6/site-packages/aplpy/normalize.py:115: RuntimeWarning: invalid value encountered in less
  negative = result < 0.
INFO: Auto-setting vmin to  3.739e-03 [aplpy.core]
INFO: Auto-setting vmax to  3.337e-02 [aplpy.core]

Polarized Intensity $I_p$¶

Level 4 HAWC+ additionally provides extensions with the polarization percentage ($p$), angle ($\theta$), and their associated errors ($\sigma$).

Percent polarization ($p$) and error ($\sigma_p$) are calculated as:

\begin{align} p & = 100\sqrt{\left(\frac{Q}{I}\right)^2+\left(\frac{U}{I}\right)^2} \\ \sigma_p & = \frac{100}{I}\sqrt{\frac{1}{(Q^2+U^2)}\left[(Q\,\sigma_Q)^2+(U\,\sigma_U)^2+2QU\,\sigma_{QU}\right]+\left[\left(\frac{Q}{I}\right)^2+\left(\frac{U}{I}\right)^2\right]\sigma_I^2-2\frac{Q}{I}\sigma_{QI}-2\frac{U}{I}\sigma_{UI}} \end{align}

Note that $p$ here represents the percent polarization as opposed to the more typical convention for $p$ as the fractional polarization.

Maps of these data are found in extensions 7 (PERCENT POL) and 9 (ERROR PERCENT POL).

Polarized intensity, $I_p$, can then be calculated as $I_p = \frac{I\times p}{100}$, which is included in extension 13 (POL FLUX).

Also included is the debiased polarization percentage ($p^\prime$) calculated as:

$p^\prime=\sqrt{p^2-\sigma_p^2}$, found in extension 8 (DEBIASED PERCENT POL).

We similarly define the debiased polarized intensity as $I_{p^\prime} = \frac{I\times p^\prime}{100}$, which is included in extension 15 (DEBIASED POL FLUX).

In [5]:
stokes_ip = hawc['DEBIASED POL FLUX']

axi = FITSFigure(stokes_i, subplot=(1,2,1))
axi.show_colorscale(cmap=cmap)               # show I


axp = FITSFigure(stokes_ip, subplot=(1,2,2), figure=plt.gcf())
axp.show_colorscale(cmap=cmap)               # show Ip

# FORMATTING
axi.set_title(r'$I$')
axp.set_title(r'$I_{p^\prime}$')
axp.axis_labels.set_yposition('right')
axp.tick_labels.set_yposition('right')
axi.set_tick_labels_font(size='small')
axi.set_axis_labels_font(size='small')
axp.set_tick_labels_font(size='small')
axp.set_axis_labels_font(size='small')
INFO: Auto-setting vmin to -9.832e-02 [aplpy.core]
INFO: Auto-setting vmax to  1.698e+00 [aplpy.core]
/home/gordon/miniconda3/lib/python3.6/site-packages/aplpy/normalize.py:115: RuntimeWarning: invalid value encountered in less
  negative = result < 0.
INFO: Auto-setting vmin to -9.530e-03 [aplpy.core]
INFO: Auto-setting vmax to  1.058e-01 [aplpy.core]

Plotting Polarization Vectors¶

From the $Q$ and $U$ maps, the polarization angle $\theta$ is calculated in the standard way:

$\theta = \frac{90}{\pi}\,\mathrm{tan}^{-1}\left(\frac{U}{Q}\right)$

with associated error:

$\sigma_\theta = \frac{90}{\pi\left(Q^2+U^2\right)}\sqrt{\left(Q\sigma_Q\right)^2+\left(U\sigma_U\right)^2-2QU\sigma_{QU}}$

The angle map is stored in extension 10 (POL ANGLE), with its error in extension 12 (ERROR POL ANGLE).

However, these angles are relative to detector coordinates. The angle we are more interested in is the angle on the sky. As part of the HAWC+ reduction pipeline, $\theta$ is corrected for the vertical position angle of the instrument on the sky, the angle of the HWP plate, as well as an offset angle that is calibrated to each filter configuration. This correction angle is applied to $\theta\rightarrow\theta^\prime$ and is saved to extension 11 (ROTATED POL ANGLE). This also affects the Stokes $Q$ and $U$ parameters, and so this factor has already been rolled into the STOKES Q and STOKES U extensions (and their corresponding error maps) in the HAWC+ data cube.

We can now use the $p^\prime$ and $\theta^\prime$ maps to plot the polarization vectors. First, however, let us make a quality cut. Rather than defining a $\sigma$ cut on the polarization vectors themselves, it is more useful to define a signal-to-noise cut on total intensity, $I$, the measured the quantity.

Returning to the definition of $p$ for the moment:

$p = \frac{100\sqrt{Q^2+U^2}}{I}$

Let's assume the errors in $Q$ and $U$ are comparable such that there are no covariant (cross) terms in the error expansion. Essentially, we define a quantity $x\equiv\sqrt{Q^2+U^2}$ so that:

\begin{align} p & = \frac{100\sqrt{Q^2+U^2}}{I} = \frac{x}{I} \\ \left(\frac{\sigma_p}{p}\right)^2 & = \left(\frac{\sigma_x}{x}\right)^2 + \left(\frac{\sigma_I}{I}\right)^2 \end{align}

If $p\sim 1\%\times I$, then

\begin{align} p & = 0.01 = \frac{x}{I} \\ x & = 0.01\,I \\ \sigma_x & = 0.01\,\sigma_I \end{align}

\begin{equation*} \Rightarrow\frac{\sigma_x}{x} = \frac{\sigma_I}{I} \end{equation*}

Therefore, \begin{equation*} \left(\frac{\sigma_p}{p}\right)^2 \sim 2\,\left(\frac{\sigma_I}{I}\right)^2 \end{equation*} Inverting this, where $\frac{\sigma_x}{x}$ is the S/N of that quantity, \begin{align*} \left(\mathrm{S/N}\right)_p & \sim \frac{1}{\sqrt{2}}\,\left(\mathrm{S/N}\right)_I \\ \left(\mathrm{S/N}\right)_I & \sim \sqrt{2}\left(\mathrm{S/N}\right)_p \\ & \sim \sqrt{2}\left(\frac{p}{\sigma_p}\right) \end{align*}

One way to think about how to proceed from here is to ask, if a fractional polarization is measured $\sim1\%$, what is the maximum error we would tolerate in that quantity? For an error of $0.5\%$ we have: \begin{align} \left(\mathrm{S/N}\right)_I & \sim \sqrt{2}\left(\frac{p}{\sigma_p}\right) \sim \sqrt{2}\frac{1}{0.5\%} \\ & \sim \frac{\sqrt{2}}{0.005} \sim 283 \end{align}

So, therefore if we desire an accuracy of $\sigma_p\sim0.5\%$, we require a S/N in total intensity $I$ of $\sim283$.

We perform the following steps:

  1. use the Stokes $I$ image as the background for the vector plot
  2. perform a quality cut on Stokes $I/\sigma_I > 100$ to make a mask
  3. mask out low S/N vectors
  4. plot remaining polarization vectors
  5. add contours to better visualize changes in flux across the map
In [65]:
from astropy.io import fits
import numpy as np
from aplpy import FITSFigure

def make_polmap(filename, title=None, figure=None, subplot=(1,1,1)):
    hawc = fits.open(filename)
    p = hawc['DEBIASED PERCENT POL']    # %
    theta = hawc['ROTATED POL ANGLE']   # deg
    stokes_i = hawc['STOKES I']         # I
    error_i = hawc['ERROR I']           # error I

    # 1. plot Stokes I
    #  convert from Jy/pix to Jy/sq. arcsec
    pxscale = stokes_i.header['CDELT2']*3600  # map scale in arcsec/pix
    stokes_i.data /= pxscale**2
    error_i.data /= pxscale**2

    fig = FITSFigure(stokes_i, figure=figure, subplot=subplot)

    # 2. perform S/N cut on I/\sigma_I
    err_lim = 100
    mask = np.where(stokes_i.data/error_i.data < err_lim)

    # 3. mask out low S/N vectors by setting masked indices to NaN
    p.data[mask] = np.nan

    # 4. plot vectors
    scalevec = 0.4  # 1pix = scalevec * 1% pol          # scale vectors to make it easier to see 
    fig.show_vectors(p, theta, scale=scalevec, step=2)  # step size = display every 'step' vectors
                                                        #   step size of 2 is effectively Nyquist sampling
                                                        #   --close to the beam size

    # 5. plot contours
    ncontours = 30
    fig.show_contour(stokes_i, cmap=cmap, levels=ncontours,
                     filled=True, smooth=1, kernel='box')
    fig.show_contour(stokes_i, colors='gray', levels=ncontours,
                     smooth=1, kernel='box', linewidths=0.3)

    # Show image
    fig.show_colorscale(cmap=cmap)
    
    # If title, set it
    if title:
        fig.set_title(title)

    # Add colorbar
    fig.add_colorbar()
    fig.colorbar.set_axis_label_text('Flux (Jy/arcsec$^2$)')

    # Add beam indicator
    fig.add_beam(facecolor='red', edgecolor='black',
                 linewidth=2, pad=1, corner='bottom left')
    fig.add_label(0.02, 0.02, 'Beam FWHM',
                  horizontalalignment='left', weight='bold',
                  relative=True, size='small')

    # Add vector scale
    #   polarization vectors are displayed such that 'scalevec' * 1% pol is 1 pix long
    #   must translate pixel size to angular degrees since the 'add_scalebar' function assumes a physical scale
    vectscale = scalevec * pxscale/3600
    fig.add_scalebar(5 * vectscale, "p = 5%",corner='top right',frame=True)
    
    # FORMATTING
    fig.set_tick_labels_font(size='small')
    fig.set_axis_labels_font(size='small')
    
    return stokes_i, p, mask, fig
In [66]:
stokes_i, p, mask, fig = make_polmap(afile, title='A')
/home/gordon/miniconda3/lib/python3.6/site-packages/ipykernel_launcher.py:22: RuntimeWarning: invalid value encountered in less
INFO: Auto-setting vmin to -6.715e-02 [aplpy.core]
INFO: Auto-setting vmax to  1.160e+00 [aplpy.core]
/home/gordon/miniconda3/lib/python3.6/site-packages/aplpy/normalize.py:115: RuntimeWarning: invalid value encountered in less
  negative = result < 0.

Plotting Polarization Fraction¶

We can also plot the polarization fraction $p$ to better visualize the structure of 30 Doradus. We plot the same contours from total intensity $I$ in the background.

In [8]:
fig = FITSFigure(p)

# Show image
fig.show_colorscale(cmap=cmap)

# Plot contours
ncontours = 30
fig.show_contour(stokes_i, colors='gray', levels=ncontours,
                 smooth=1, kernel='box', linewidths=0.3)

# Add colorbar
fig.add_colorbar()
fig.colorbar.set_axis_label_text('$p$ (%)')
INFO: Auto-setting vmin to -9.345e-01 [aplpy.core]
INFO: Auto-setting vmax to  1.037e+01 [aplpy.core]
/home/gordon/miniconda3/lib/python3.6/site-packages/aplpy/normalize.py:115: RuntimeWarning: invalid value encountered in less
  negative = result < 0.

HAWC+ Polarization Maps¶

Finally, using the function defined above, we plot all four HAWC+ observations of 30 Doradus.

In [9]:
files = [afile,cfile,dfile,efile]
titles = ['A','C','D','E']

for file, title in zip(files,titles):
    make_polmap(file,title)
/home/gordon/miniconda3/lib/python3.6/site-packages/ipykernel_launcher.py:22: RuntimeWarning: invalid value encountered in less
INFO: Auto-setting vmin to -6.715e-02 [aplpy.core]
INFO: Auto-setting vmax to  1.160e+00 [aplpy.core]
/home/gordon/miniconda3/lib/python3.6/site-packages/aplpy/normalize.py:115: RuntimeWarning: invalid value encountered in less
  negative = result < 0.
INFO: Auto-setting vmin to -8.639e-02 [aplpy.core]
INFO: Auto-setting vmax to  9.343e-01 [aplpy.core]
INFO: Auto-setting vmin to -2.750e-02 [aplpy.core]
INFO: Auto-setting vmax to  3.486e-01 [aplpy.core]
INFO: Auto-setting vmin to -9.768e-03 [aplpy.core]
INFO: Auto-setting vmax to  1.171e-01 [aplpy.core]
In [57]:
hawc = fits.open(afile)
p = hawc['DEBIASED PERCENT POL']    # %
error_p = hawc['ERROR PERCENT POL'] # %
stokes_i = hawc['STOKES I']         # I
error_i = hawc['ERROR I']           # error I

#  convert from Jy/pix to Jy/sq. arcsec
pxscale = stokes_i.header['CDELT2']*3600  # map scale in arcsec/pix
stokes_i.data /= pxscale**2
error_i.data /= pxscale**2

# make S/N cut on stokes i
err_lim = 283
mask = np.where(stokes_i.data/error_i.data < err_lim)

# mask out low S/N vectors by setting masked indices to NaN
p.data[mask] = np.nan
p.data[p.data<0.1] = np.nan
/home/gordon/miniconda3/lib/python3.6/site-packages/ipykernel_launcher.py:14: RuntimeWarning: invalid value encountered in less
  
/home/gordon/miniconda3/lib/python3.6/site-packages/ipykernel_launcher.py:18: RuntimeWarning: invalid value encountered in less
In [58]:
plt.figure()
plt.errorbar(stokes_i.data.flatten(),p.data.flatten(),
             yerr=error_p.data.flatten(),
             xerr=error_i.data.flatten(),
             fmt='k.')

plt.xlabel('Stokes I (Jy/arcsec$^2$)')
plt.ylabel('$p$ (%)')
Out[58]:
Text(0, 0.5, '$p$ (%)')
In [59]:
plt.figure()
plt.scatter(p.data.flat,error_p.data.flat)
Out[59]: